NAIROBI, Kenya (CNN) -- Uhuru Kenyatta, indicted for alleged crimes against humanity and the son of Kenya"s founding father, had an early lead Wednesday in the presidential election.

With a little more than 40 percent of the vote counted, Kenyatta was ahead at 53 percent to 42 percent over his main rival, Prime Minister Raila Odinga, according to the election commission website.

If Kenyatta wins, he will find himself in an unusual quandary.

He has been indicted by the International Criminal Court for allegedly inciting a local militia to conduct reprisal attacks in the last election.

His running mate, William Ruto, also faces ICC charges at The Hague. Both have denied the charges.

Kenyatta said that if he is elected, the indictment will not affect his ability to do his job.

"I don"t think that"s an issue that anybody should be concerned with," said Kenyatta, a deputy prime minister. "I have been a member of the government and I"ve still been able to execute my duties. I still believe I will be able to execute my duties as president once selected."

The international community should respect the will of Kenyans, he said.

"If they do decide it"s me, that"s a domestic issue left to the sovereign democratic will of the people of Kenya," he said last week. "Any friend of Kenya must recognize that and must take it in their stride."

"Skype government"

But Odinga has raised concerns about the indictment, saying his opponent plans to run a "Skype government" from The Hague.

Kenyatta has maintained a lead since polls closed after Monday"s election, but it is still too early to declare a winner.

Analysts have raised the possibility of a runoff.

The election carries significance far beyond its borders.

As the largest economy in East Africa, Kenya is a crucial trade route into the rest of the continent and provides an important buffer of stability in a region that includes the fledgling Somali government and the politically tense Sudan and South Sudan.

Kenya is also a major U.S. ally in the war against Islamist militants in the region and has remained relatively peaceful amid civil wars in neighboring nations.

"Hiccups here and there"

As Kenyans eagerly await the outcome, glitches with the new electronic voter system are affecting the tallying, officials said.

Counting has slowed down after the electronic systems failed, forcing officers to manually deliver paper copies of vote tallies, according to Odinga"s campaign team.

The election commission urged citizens to be calm and patient, hoping to avoid tension and distrust in the system, which contributed to post-election violence in December 2007.

"Sometimes a couple of computers would get kind of out of whack and would slow the process down," said Abdullahi Sharawi, a commissioner of Kenya"s Independent Electoral and Boundaries Commission.

"Definitely, there is going to be some hiccups here and there, but I think, when you assess the whole, then we think the work, so far, is very good," he said.

United Nations chief Ban Ki-moon urged Kenyans to maintain peace.

"I have been encouraged thus far by the largely peaceful and orderly process, despite some incidents of violence and some technical problems," he said.

Eager to avoid violence

Kenyans are eager to avoid a repeat of the 2007 election.

At the time, the nation plunged into ethnic violence after Odinga disputed results that declared the incumbent president, Mwai Kibaki, as the winner, alleging the election had been rigged.

Protesters took to the streets, where supporters of both camps fought one another.

More than 1,200 people were killed and hundreds of thousands displaced -- the worst violence since the nation gained independence. Clashes ended with the formation of a power-sharing government with Kibaki as president and Odinga as prime minister.

While the poll has been relatively peaceful this time, authorities said at least 10 people were killed in isolated incidents on the coast.

Complicated election

Leading up to this election, the candidates declared they would settle any voting disputes in court and urged their supporters to avoid bloodshed at all costs.

After the 2007 voting disaster, the government set up an ambitious new constitution, making this election one of the nation"s most complicated polls since the country gained independence from Britain in 1963.

It also revamped various political systems, including the electoral process and the judicial system.

But analysts say the real test will come after the results are announced: Will the loser bow out gracefully to avoid stoking tensions?

Millions cast ballots

About 70 percent of the 14.3 million eligible voters voted this week, according to election officials. Eight contenders are vying for the presidency.

The winner must secure more than 50 percent of the vote to avoid a runoff tentatively scheduled for next month.